S189: PROTEOGENOMIC LANDSCAPE OF MULTIPLE MYELOMA
Authors: Evelyn Ramberger, Anna Dolnik, Yuen Lam Dora Ng, Matthias Ziehm, Oliver Popp, Eric Sträng, Miriam Kull, Valeriia Sapozhnikova, Florian Grünschläger, Manuela Benary, Sina Müller, Xiang Gao, Arunima Murgai, Mohamed Haji, Annika Schmidt, Raphael Lutz, Axel Nogai, Jan Braune, Dominik Laue, Christian Langer, Cyrus Khandanpour, Florain Bassermann, Hartmut Döhner, Monika Engelhardt, Christian Straka, Michael Hundemer, Simon Haas, Dieter Beule, Ulrich Keller, Hermann Einsele, Lars Bullinger, Stefan Knop, Philipp Mertins, Jan Krönke
Journal: HemaSphere (2023)

Background: Multiple myeloma is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, it remains incurable and better risk stratification as well as new therapies are therefore highly needed. While genomic alterations and gene expression profiles have been extensively studied that led to new insights into disease biology and improved prognostic models, the proteome of multiple myeloma has not been systematically assessed. Aims: To provide a comprehensive multi-omics analysis of plasma cell malignancies. Methods: Samples from 138 patients with plasma cell malignancies including 114 cases of newly diagnosed multiple myeloma treated within trials of the German Study Group Multiple Myeloma (DSMM) with available clinical data, were analyzed by deep tandem mass tags (TMT)-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing. Results: TMT-based proteomics of multiple myeloma samples identified a total of 8,336 proteins and 25,131 phosphopeptides in at least half of the samples. Among the highly expressed proteins were established markers of multiple myeloma including the transcription factor IRF4, and cell-surface proteins CD38 and CD138. Primary genetic events had profound effects on the expression levels of proteins in cis and trans. Most significant proteins and phosphopeptides in the mutually exclusive genetic subtypes of multiple myeloma include the translocation partners CCND1 in cases with t(11;14) with subsequent increase of CDK4 and RB1 phosphorylation and NSD2 in cases with t(4;14), as well as proteins upregulated specifically in hyperdiploid myeloma, such as USP4 (Chr 3p) and PKM (Chr 15q). However, protein levels and activity could not necessarily be inferred by genetic alterations or RNA expression which may affect targeted therapy approaches in multiple myeloma. For example, FGFR3, the second translocation partner in t(4;14) cases, could only be detected in 63% of cases with t(4;14) and vice versa also non-t(4;14) cases had above average FGFR3 expression. FGFR3 protein expression was highly associated with FGFR3 signaling and in myeloma cell lines FGFR3 expression predicted sensitivity to FGFR3 inhibition. MCL1, which is encoded on chr 1q and currently being investigated as a therapeutic target in multiple myeloma in clinical trials, was elevated in only 70% of cases with 1q gain but also in 34% of patients without a detected 1q alteration. Cases with t(11;14) had extensive deregulation of proteins involved in the apoptotic pathway and B-cell markers which may be linked to the particular sensitivity to BCL2 inhibition of this subgroup. Comparison with the proteome of plasma cells and hematopoietic progenitor cells isolated from healthy donors and integration with CRISPR/Cas9 screens revealed new potential disease drivers and therapeutic targets of multiple myeloma. In addition, we found surface proteins with selective expression on multiple myeloma cells as compared to healthy bone marrow cells which could be confirmed by single-cell RNA sequencing. Correlation of protein and phosphopeptide levels with outcome revealed a protein high-risk signature consisting of eight proteins that is highly predictive for progression-free and overall survival in intensively treated patients and independent of cytogenetic-based risk stratification. This high-risk signature was furthermore enriched in plasma-cell leukemia, the most aggressive plasma cell malignancy. Summary/Conclusion: Our findings provide new insights in the biology of multiple myeloma and highlight the broad implications of proteomics studies in hematologic malignancies.Keywords: Proteomics, Myeloma, Multiple myeloma